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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgtagccacatagatgttggtcatagtttctgcaggtcttttagcttatgtttcctagtttgattgtaaggagctggacgttgttgtggctggctattttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtattagGTTGGCTTGCCTGCTCGAGGAAAGACTTTTACTGCAGCAAAGTTGACAAGATATCTACGCTGGTTGGGACATGATACTAAACATTTTAATGTTGGAAAG

Basic information

species Arabidopsis thaliana
transcript AT1G07110.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
gtatttgtagccacatagatgttggtcatagtttctgcaggtcttttagcttatgtttcctagtttgattgtaaggagctggacgttgttgtggctggctattttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtattagGTTGGCTTGCCTGCTCGAGGAAAGACTTTTACTGCAGCAAAGTTGACAAGATATCTACGCTGGTTGGGACATGATACTAAACATTTTAATGTTGGAAAG
                                                                            |||||||   | ||   | |      || |  |  |||     | |   |  | | ||  |   |   |      |||||  ||   | |||  | |   | |||    ||||||||  | || |||||||| ||||| ||||| ||||| ||  | ||||||||||| || ||||| || ||||| || ||||| || ||||||||||||
----------------------------------------------------------------------------agctgga-actattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgca------gttctttttttaatcat--ctgctgatatt---ctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG

upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
gtatttgtagccacatagatgttggtcatagtttctgcaggtcttttagcttatgtttcctagtttgattgtaaggagctggacgttgttgtggctggctattttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtatt--agGTTGGCTTGCCTGCTCGAGGAAAGACTTTTACTGCAGCAAAGTTGACAAGATATCTACGCTGGTTGGGACATGATACTAAACATTTTAATGTTGGAAAG
                                                                                | |  ||   ||  |  ||   || |||  | || |         || |   |||||   |   ||    | |  | |     |    |     |||| || ||||  ||||||||||||| |||||||| || |||||||||||||| ||  | ||||||||||| ||||||||||| ||||| || ||||| || ||||||||||||
--------------------------------------------------------------------------------gcaacttccagtaac-agcaggttaattccatttgt---------tgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaacaaatttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG

upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S235_92V6.1 (Physcomitrella patens), 3'ss of exon 5
gtatttgtagccacatagatgttggtcatagtttctgcaggtcttttagcttatgtttcctagtttgattgtaaggagctggacgttgttgtggctggctattt-tatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtattagGTTGGCTTGCCTGCTCGAGGAAAGACTTTTACTGCAGCAAAGTTGACAAGATATCTACGCTGGTTGGGACATGATACTAAACATTTTAATGTTGGAAAG
                                                                                         |    |   ||  ||  |||  |    |||     | ||    |||| |  | |             || | || ||    |  ||||   | |  | |||||||| | ||||||||||| ||||||||||| ||||| ||| |||| ||||||||  | ||| | || |||||||| ||||| || ||||||||||||
-----------------------------------------------------------------------------------------tacaacgaacttcttacattacaagcttaagttcgactgcttgaaaatatcatagcttcttcaagcatgttacatactgaacttgtcatggtggattcagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG

upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S414_24V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatttgtagccacatagatgttggtcatagtttctgcaggtcttttagcttatgtttcctagtttgattgtaaggagctggacgttgttgtggc-tggctattttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcac--accattcccgtcaaaattgtattagGTTGGCTTGCCTGCTCGAGGAAAGACTTTTACTGCAGCAAAGTTGACAAGATATCTACGCTGGTTGGGACATGATACTAAACATTTTAATGTTGGAAAG
                                                                                             ||  |  ||    | || |   | || |||  ||     |    |||| |        | ||   | | ||  | | | |  ||     | |  | ||||||| || ||||| ||||| ||||| ||||| |||||||| ||||| ||||||||  | ||| | || |||||||||||||| || ||||||||||| 
-------------------------------------------------------------------------------------------cagcgcgattaaacgaattgaagcagaagcgtcgatttttcatgtgaaaatattggaatttctttcaaataactcatcctactggttgctttgggttcagGTTGGGTTACCTGCACGAGGCAAGACGTTTACGGCAGCAAAATTGACGAGATATCTTAGGTGGCTAGGCCATGATACTAAACACTTCAATGTTGGAAAA

upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ11749 (Selaginella moellendorffii), 3'ss of exon 1
gtatttgtagccacatagatgttggtcatagtttctgcaggtcttttagcttatgtttcctagtttgattgtaaggagctggacgttgttgtggctggctattttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtatt---agGTTGGCTTGCCTGCTCGAGGAAAGACTTTTACTGCAGCAAAGTTGACAAGATATCTACGCTGGTTGGGACATGATACTAAACATTTTAATGTTGGAAAG
                                                                                                                                   |    | |   | |  |  |  |   | ||     | | | |  |    ||  ||   ||||||||||||||||  |||| || || |||||||| || |||||||| |||||  |||| ||| ||||||||||||| || || || || |||||||||
---------------------------------------------------------------------------------------------------------------------------------gtacgctagagcgaaatcgtcttctaccactctgttaaattctgggattcgtgcctttccagGTTGGCTTGCCTGCGAGAGGGAAAACGTTTACTGCCGCGAAGTTGACGAGATACTTACGTTGGCTGGGACATGATACCAAGCACTTCAACGTTGGAAAG

upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ22544 (Selaginella moellendorffii), 3'ss of exon 1
gtatttgtagccacatagatgttggtcatagtttctgcaggtcttttagcttatgtttcctagtttgattgtaaggagctggacgttgttgtggctggctattttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccg--tcaaaattgtattagGTTGGCTTGCCTGCTCGAGGAAAGACTTTTACTGCAGCAAAGTTGACAAGATATCTACGCTGGTTGGGACATGATACTAAACATTTTAATGTTGGAAAG
                                                                                                                                  |    | |   ||  ||   | | |   |       ||||  |  |        |   ||||||||||||||||  |||| || || |||||||| || |||||||| |||||  |||| ||| ||||||||||||| || || || || |||||||||
--------------------------------------------------------------------------------------------------------------------------------gtacgctagagcgaaatcttcttctaccactctgttaaattctgggattcgtgcctttccagGTTGGCTTGCCTGCGAGAGGGAAAACGTTTACTGCCGCGAAGTTGACGAGATACTTACGTTGGCTGGGACATGATACCAAGCACTTCAACGTTGGAAAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|125212454|gb|EL227408.1|EL227408
EST:     TAGCAATTGTCCTG                         GTTGGCTTGCCTGCTCGAGGAAAGACTTTTACTGCAGCAAAGTTGACAAGA
genomic: TAGCAATTGTCCTGgtatttgtag ... attgtattagGTTGGCTTGCCTGCTCGAGGAAAGACTTTTACTGCAGCAAAGTTGACAAGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtattagGTTGGCTTGCCTGCTCGAGGAAAGACTTTTACTGCAGCAAAGTTGACAAGATATCTACGCTGGTTGGGACATGATACTAAACATTTTAATGTTGGAAAG
                   ttctgat  putative branch site (score: 3)
                                        tcaaaattgtatta  TA-rich tract